Working out in the morning will raise your base metabolism for the rest of the day, so overall you will burn more calories.
Having said that, in the long run, the key to weight loss is consistency, so its better to do something every day, at whatever time, than work out in the morning twice a week.
Doing it and enjoying it is the important thing. It is also a question of habit, and they take time to change. You say you dont have much time in the morning, and that may be the case.
From experience, I do feel a sense of satisfaction when I've made the effort to get up early and do a workout, so that by the time I've got to work I feel I've got a head start on everyone else and done something useful.